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- PDB-4g6a: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g6a | ||||||
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Title | Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody AP33 | ||||||
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![]() | IMMUNE SYSTEM / Immunoglobulin Fold | ||||||
Function / homology | ![]() host cell lipid droplet / lipid droplet / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kong, L. / Wilson, I.A. / Law, M. | ||||||
![]() | ![]() Title: Structure of Hepatitis C Virus Envelope Glycoprotein E2 Antigenic Site 412 to 423 in Complex with Antibody AP33. Authors: Kong, L. / Giang, E. / Nieusma, T. / Robbins, J.B. / Deller, M.C. / Stanfield, R.L. / Wilson, I.A. / Law, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.9 KB | Display | ![]() |
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PDB format | ![]() | 146.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.8 KB | Display | ![]() |
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Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dgvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 1554.710 Da / Num. of mol.: 2 / Fragment: E2 peptide / Source method: obtained synthetically Details: this sequence naturally occurs in Hepatitis C virus Source: (synth.) ![]() #2: Antibody | Mass: 24103.893 Da / Num. of mol.: 2 / Fragment: antibody Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 23711.229 Da / Num. of mol.: 2 / Fragment: antibody Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 17% (w/v) PEG 4000, 8.5% (v/v) 2-propanol, 15% (v/v) glycerol and 0.085 M Sodium HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.97 Å / Num. all: 29450 / Num. obs: 29450 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 61.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DGV Resolution: 2.501→47.97 Å / SU ML: 0.65 / σ(F): 1.43 / Phase error: 24.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.244 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.501→47.97 Å
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Refine LS restraints |
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LS refinement shell |
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